An online resource for data mining of processed DNA sequence databases
PipeOnline is an experimental Web-based resource designed by the OSU Bioinformatics Group to assist investigators in the determination of metabolic and biological function from large-scale DNA sequence data. Databases include public cDNA sequences from several fungal and plant model organisms. Data were processed automatically using PipeOnline v2.00 which contains a series of script-linked programs that process multiple (up to several thousand) raw DNA sequence files and to produce a database of records that can be retrieved through a series of specific queries or through a comprehensive gene-function browser (Fig 1). Briefly, PipeOnline produces a new set of contig-assembled files assembled using phrap. Assembled sequences were compared against a local NCBI non-redundant peptide sequence database using blastx. The resulting output files are automatically collected, parsed, formatted, assembled, indexed and uploaded to a local MySQL server by the PipeOnline database assembly module. Functional sorting of the input DNA sequences is achieved through a proprietary sorting method that utilizes functional information gathered from public databases.. Function has been estimated using the functional dictionary MPW Metabolic Pathways Database obtained from WIT. Records in each database can be reached by browsing a functional overview of each database or by query of key words such as record name or description of protein sequence alignments from blastx analysis. Retrieved PipeOnline records can also be downloaded in various formats (TAB and FASTA) for local use.
How to cite PipeOnline:
Ayoubi, P, Jin X, Leite S, Liu X, Martajaja J, Abduraham A, Wan Q, Yan W, Misawa E and Prade RA. 2002. PipeOnline 2.0: automated EST processing and functional data sorting. Nucleic Acids Research. 30:4761-4769. Abstract
